[BioC] Regression using LIMMA

[Naomi Altman]

Without the model it is hard to say, but I am guessing you fitted a 
straight line for each gene.  So the intercept is the intercept of 
the line, and the coefficient for dose is the slope.  The t-stat is 
the test of whether the intercept and slope are equal zero.  The 
intercept is not interesting for your purpose.  The slope tells you 
if there is a statistically significant dose effect.

Regards,
Naomi


At 07:17 PM 11/9/2010, somnath bandyopadhyay wrote:

>Hi there,
>I am trying to use LIMMA to analyze gene expression data from an 
>experiment which has dose response but only one replicate at each 
>dose. I tried to fit a linear model using lmfit(). I used the doses 
>as continuous variable. I do the ebayes fit and finally do decide 
>tests with adj p values (BH corrected). I get coefficients, 
>intercept and dose as output with t-stat and p values for each. I 
>was wondering how to interpret these. What does intercept, dose and 
>coefficients mean in this case? The data matrix I read into R was 
>Affy Plus2 chip data for 4 doses of a compound. Any help would be 
>greatly appreciated.
>Best Regards,Som.
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